v0.6.3

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Reformat code style with Black
+0f830f2ddb23f21bd6e986f6b5c9ba05d6b0fa17

.github/workflows/running_linter.yml

@@ -0,0 +1,15 @@
+# This workflow will run ruff to highlight syntactical and stylistic problems.
+
+name: Running Ruff
+
+on: [push]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1

.github/workflows/running_test.yml

@@ -0,0 +1,44 @@
+# This workflow will run unit tests with pytest and upload reports to codecov.
+
+name: Running test
+
+on: [push]
+
+jobs:
+
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        include:
+          - os: ubuntu-20.04
+            python-version: "3.6"
+          - os: ubuntu-20.04
+            python-version: "3.7"
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements_dev.txt
+      - name: List dependencies
+        run: pip list
+      - name: Run tests and collect coverage
+        run: |
+          pytest --cov=./
+      - name: Upload coverage reports to Codecov
+        run: |
+          curl -Os https://uploader.codecov.io/latest/linux/codecov
+          chmod +x codecov
+          ./codecov -t ${CODECOV_TOKEN}

.github/workflows/upload_package.yml

@@ -0,0 +1,50 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Upload Python package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  build-n-publish:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: |
+          rm -r build/*
+          rm -r dist/*
+          python -m build
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: arthur_imbert
+          password: ${{ secrets.PYPI_TOKEN_BIGFISH }}
+
+
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: arthur_imbert
+          password: ${{ secrets.PYPI_API_TOKEN }}

CITATION.cff

@@ -0,0 +1,51 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Imbert"
+  given-names: "Arthur"
+- family-names: "Ouyang"
+  given-names: "Wei"
+- family-names: "Safieddine"
+  given-names: "Adham"
+- family-names: "Coleno"
+  given-names: "Emeline"
+- family-names: "Zimmer"
+  given-names: "Christophe"
+- family-names: "Bertrand"
+  given-names: "Edouard"
+- family-names: "Walter"
+  given-names: "Thomas"
+- family-names: "Mueller"
+  given-names: "Florian"
+title: "FISH-quant v2: a scalable and modular tool for smFISH image analysis"
+doi: 10.1261/rna.079073.121
+date-released: 2022-03
+url: "https://github.com/fish-quant/big-fish"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Imbert"
+    given-names: "Arthur"
+  - family-names: "Ouyang"
+    given-names: "Wei"
+  - family-names: "Safieddine"
+    given-names: "Adham"
+  - family-names: "Coleno"
+    given-names: "Emeline"
+  - family-names: "Zimmer"
+    given-names: "Christophe"
+  - family-names: "Bertrand"
+    given-names: "Edouard"
+  - family-names: "Walter"
+    given-names: "Thomas"
+  - family-names: "Mueller"
+    given-names: "Florian"
+  doi: 10.1261/rna.079073.121
+  journal: "RNA"
+  month: 3
+  start: 786
+  end: 795
+  title: "FISH-quant v2: a scalable and modular tool for smFISH image analysis"
+  issue: 6
+  volume: 28
+  year: 2022

README.md

@@ -1,11 +1,13 @@
 # Big-FISH
 
 [![PyPI version](https://badge.fury.io/py/big-fish.svg)](https://badge.fury.io/py/big-fish)
-[![Build Status](https://travis-ci.com/fish-quant/big-fish.svg?branch=master)](https://travis-ci.com/fish-quant/big-fish)
+[![Running test](https://github.com/fish-quant/big-fish/actions/workflows/running_test.yml/badge.svg)](https://github.com/fish-quant/big-fish/actions/workflows/running_test.yml)
 [![Documentation Status](https://readthedocs.org/projects/big-fish/badge/?version=stable)](https://big-fish.readthedocs.io/en/latest/?badge=stable)
 [![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg)](https://codecov.io/gh/fish-quant/big-fish)
 [![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
 [![Python version](https://img.shields.io/pypi/pyversions/big-fish.svg)](https://pypi.python.org/pypi/big-fish/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 **Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.
 
@@ -28,19 +30,21 @@ Big-FISH requires Python 3.6 or newer. Additionally, it has the following depend
 - mrc (>= 0.1.5)
 
 For segmentation purpose, two additional dependencies can be requested:
-- tensorflow (== 2.3.0)
-- tensorflow-addons (== 0.12.1)
+- tensorflow (>= 2.3.0)
+- tensorflow-addons (>= 0.12.1)
 
 ### Virtual environment
 
-To avoid dependency conflicts, we recommend the the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment.  In a terminal run the command:
+To avoid dependency conflicts, we recommend the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment.  In a terminal run the command:
 
 ```bash
-conda create -n bigfish_env python=3.6
+conda create -n bigfish_env python=X.Y
 source activate bigfish_env
 ```
 
-We recommend two options to then install Big-FISH in your virtual environment.
+With X.Y a valid Python version greater or equal than 3.6. Note that Big-FISH has been tested for Python 3.6, 3.7, 3.8, 3.9 and 3.10.
+
+We then recommend two options to install Big-FISH in your virtual environment: from PyPi or GitHub.
 
 #### Download the package from PyPi
 
@@ -50,9 +54,9 @@ Use the package manager [pip](https://pip.pypa.io/en/stable/) to install Big-FIS
 pip install big-fish
 ```
 
-#### Clone package from Github
+#### Clone the package from GitHub
 
-Clone the project's [Github repository](https://github.com/fish-quant/big-fish) and install it manually with the following commands:
+Clone the project's [GitHub repository](https://github.com/fish-quant/big-fish) and install it manually with the following commands:
 
 ```bash
 git clone [email protected]:fish-quant/big-fish.git
@@ -68,7 +72,7 @@ This package is part of the [FISH-Quant](https://fish-quant.github.io/) framewor
 
 ## Support
 
-If you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/big-fish/issues). You can also contact [Arthur Imbert](mailto:arthur.imbert@mines-paristech.fr) or [Florian Mueller](mailto:[email protected]).
+If you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/big-fish/issues). You can also contact [Arthur Imbert](mailto:arthur.imbert[email protected]) or [Florian Mueller](mailto:[email protected]).
 
 ## Roadmap (suggestion)
 
@@ -91,7 +95,7 @@ git checkout develop
 
 ### Contributing
 
-[Pull requests](https://github.com/fish-quant/big-fish/pulls) are welcome. For major changes, please open an [issue](https://github.com/fish-quant/big-fish/issues) first to discuss what you would like to change.
+[Pull requests](https://github.com/fish-quant/big-fish/pulls) on the `develop` branch are welcome. For major changes, please open an [issue](https://github.com/fish-quant/big-fish/issues) first to discuss what you would like to change.
 
 ### Testing
 
@@ -107,8 +111,23 @@ To perform unit tests, run :
 pytest bigfish
 ```
 
-## Citation
+## Bibtex citation
 
 If you exploit this package for your work, please cite:
 
-> Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024
+```bibtex
+@article{Imbert2022,
+    author  = {Imbert, Arthur and Ouyang, Wei and Safieddine, Adham and 
+               Coleno, Emeline and Zimmer, Christophe and 
+               Bertrand, Edouard and Walter, Thomas and Mueller, Florian},
+    doi     = {10.1261/rna.079073.121},
+    journal = {RNA},
+    month   = mar,
+    number  = {6},
+    pages   = {786--795},
+    title   = {{FISH-quant v2: a scalable and modular tool for smFISH image 
+                analysis}},
+    volume  = {28},
+    year    = {2022}
+}
+```

bigfish/__init__.py

@@ -12,4 +12,4 @@
 # MINOR: new features
 # PATCH: backwards compatible bug fixes
 # MAJOR.MINOR.PATCHdev means a version under development
-__version__ = "0.6.2"
+__version__ = "0.6.3dev"

bigfish/classification/__init__.py

@@ -21,8 +21,7 @@
 from .features import features_centrosome
 
 
-_input_preparation = [
-    "prepare_extracted_data"]
+_input_preparation = ["prepare_extracted_data"]
 
 _features = [
     "compute_features",
@@ -34,6 +33,7 @@
     "features_topography"
     "features_foci"
     "features_area"
-    "features_centrosome"]
+    "features_centrosome",
+]
 
 __all__ = _input_preparation + _features